def test_nisin(self):
"Test lanthipeptide prediction for nisin A"
rec = Record.from_biopython(seqio.read(
helpers.get_path_to_nisin_with_detection()),
taxon="bacteria")
assert not rec.get_cds_motifs()
result = run_specific_analysis(rec)
assert len(result.clusters) == 1
motifs = self.gather_all_motifs(result)
assert len(motifs) == 1
assert not rec.get_cds_motifs()
result.add_to_record(rec)
assert len(rec.get_cds_motifs()) == 1
prepeptide = motifs[0]
# real monoisotopic mass is 3351.51, but we overpredict a Dha
self.assertAlmostEqual(3333.6,
prepeptide.monoisotopic_mass,
delta=0.05)
# real mw is 3354.5, see above
self.assertAlmostEqual(3336.0, prepeptide.molecular_weight, delta=0.05)
for expected, calculated in zip([3354.0, 3372.1, 3390.1, 3408.1],
prepeptide.alternative_weights):
self.assertAlmostEqual(expected, calculated, delta=0.05)
assert prepeptide.lan_bridges == 5
self.assertEqual("MSTKDFNLDLVSVSKKDSGASPR", prepeptide.leader)
self.assertEqual("ITSISLCTPGCKTGALMGCNMKTATCHCSIHVSK", prepeptide.core)
self.assertEqual('Class I', prepeptide.peptide_subclass)
initial_json = result.to_json()
regenerated = LanthiResults.from_json(initial_json, rec)
assert list(result.motifs_by_locus) == ["nisB"]
assert str(result.motifs_by_locus) == str(regenerated.motifs_by_locus)
assert result.clusters == regenerated.clusters
assert initial_json == regenerated.to_json()
def test_labyrinthopeptin(self):
"Test lanthipeptide prediction for labyrinthopeptin"
filename = path.get_full_path(__file__, 'data', 'labyrinthopeptin.gbk')
rec = Record.from_biopython(seqio.read(filename), taxon="bacteria")
assert not rec.get_cds_motifs()
result = run_specific_analysis(rec)
motifs = self.gather_all_motifs(result)
assert len(motifs) == 2
assert not rec.get_cds_motifs()
result.add_to_record(rec)
assert len(rec.get_cds_motifs()) == 2
def test_sco_cluster3(self):
"Test lanthipeptide prediction for SCO cluster #3"
filename = path.get_full_path(__file__, 'data', 'sco_cluster3.gbk')
rec = Record.from_biopython(seqio.read(filename), taxon="bacteria")
assert not rec.get_cds_motifs()
result = run_specific_analysis(rec)
motifs = self.gather_all_motifs(result)
assert len(motifs) == 1
assert not rec.get_cds_motifs()
result.add_to_record(rec)
assert len(rec.get_cds_motifs()) == 1
self.assertEqual('Class I', motifs[0].peptide_subclass)
def test_lactocin_s(self):
"""Test lanthipeptide prediction for lactocin S"""
filename = path.get_full_path(__file__, 'data', 'lactocin_s.gbk')
rec = Record.from_biopython(seqio.read(filename), taxon="bacteria")
assert not rec.get_cds_motifs()
result = run_specific_analysis(rec)
assert len(result.clusters) == 1
assert result.clusters[1] == set(["lasM"])
assert len(result.motifs_by_locus["lasM"]) == 1
motifs = result.motifs_by_locus["lasM"]
assert len(motifs) == 1
assert not rec.get_cds_motifs()
result.add_to_record(rec)
assert len(rec.get_cds_motifs()) == 1
self.assertEqual('Class II', motifs[0].peptide_subclass)
def test_multiple_biosynthetic_enzymes(self):
filename = path.get_full_path(__file__, 'data',
'CP013129.1.section.gbk')
rec = record_processing.parse_input_sequence(filename,
taxon="bacteria")[0]
rec.clear_cds_motifs()
assert rec.get_cluster(0).products == ("lanthipeptide", "nrps")
assert rec.get_cluster(0).cds_children
result = run_specific_analysis(rec)
assert len(result.clusters) == 1
assert result.clusters[1] == set(["AQF52_7190", "AQF52_7168"])
motif = result.motifs_by_locus["AQF52_7190"][0]
assert motif.peptide_subclass == "Class II"
motif = result.motifs_by_locus["AQF52_7168"][0]
assert motif.peptide_subclass == "Class III"
def test_epidermin(self):
"Test lanthipeptide prediction for epidermin"
filename = path.get_full_path(__file__, 'data', 'epidermin.gbk')
rec = Record.from_biopython(seqio.read(filename), taxon="bacteria")
assert not rec.get_cds_motifs()
result = run_specific_analysis(rec)
motifs = self.gather_all_motifs(result)
assert len(motifs) == 1
assert not rec.get_cds_motifs()
result.add_to_record(rec)
assert len(rec.get_cds_motifs()) == 1
prepeptide = motifs[0]
self.assertAlmostEqual(2164, prepeptide.monoisotopic_mass, delta=0.5)
self.assertAlmostEqual(2165.6, prepeptide.molecular_weight, delta=0.5)
self.assertEqual(3, prepeptide.lan_bridges)
self.assertEqual("MEAVKEKNDLFNLDVKVNAKESNDSGAEPR", prepeptide.leader)
self.assertEqual("IASKFICTPGCAKTGSFNSYCC", prepeptide.core)
self.assertEqual('Class I', prepeptide.peptide_subclass)
self.assertEqual(['AviCys'], prepeptide.get_modifications())
def test_epicidin(self):
"Test lanthipeptide prediction for epicidin 280"
filename = path.get_full_path(__file__, 'data', 'epicidin_280.gbk')
rec = Record.from_biopython(seqio.read(filename), taxon="bacteria")
assert len(rec.get_cds_motifs()) == 1
result = run_specific_analysis(rec)
motifs = self.gather_all_motifs(result)
assert len(motifs) == 1
assert len(rec.get_cds_motifs()) == 1
result.add_to_record(rec)
assert len(rec.get_cds_motifs()) == 2
prepeptide = motifs[0]
self.assertAlmostEqual(3115.7, prepeptide.monoisotopic_mass, delta=0.5)
self.assertAlmostEqual(3117.7, prepeptide.molecular_weight, delta=0.5)
for expected, calculated in zip([3135.7, 3153.7, 3171.7],
prepeptide.alternative_weights):
self.assertAlmostEqual(expected, calculated, delta=0.05)
self.assertEqual(3, prepeptide.lan_bridges)
self.assertEqual("MENKKDLFDLEIKKDNMENNNELEAQ", prepeptide.leader)
self.assertEqual("SLGPAIKATRQVCPKATRFVTVSCKKSDCQ", prepeptide.core)
self.assertEqual('Class I', prepeptide.peptide_subclass)
self.assertEqual(['Lac'], prepeptide.get_modifications())
def test_microbisporicin(self):
"Test lanthipeptide prediction for microbisporicin"
filename = path.get_full_path(__file__, 'data', 'microbisporicin.gbk')
rec = Record.from_biopython(seqio.read(filename), taxon="bacteria")
assert not rec.get_cds_motifs()
result = run_specific_analysis(rec)
motifs = self.gather_all_motifs(result)
assert len(motifs) == 1
assert not rec.get_cds_motifs()
result.add_to_record(rec)
assert len(rec.get_cds_motifs()) == 1
prepeptide = motifs[0]
# NOTE: this is not the correct weight for microbisporicin
# there are some additional modifications we do not predict yet
self.assertAlmostEqual(2212.9, prepeptide.monoisotopic_mass, delta=0.5)
self.assertAlmostEqual(2214.5, prepeptide.molecular_weight, delta=0.5)
self.assertEqual(4, prepeptide.lan_bridges)
self.assertEqual("MPADILETRTSETEDLLDLDLSIGVEEITAGPA",
prepeptide.leader)
self.assertEqual("VTSWSLCTPGCTSPGGGSNCSFCC", prepeptide.core)
self.assertEqual('Class I', prepeptide.peptide_subclass)
self.assertEqual(['AviCys', 'Cl', 'OH'],
prepeptide.get_modifications())